MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0512 b0871 b2779 b2925 b2097 b0030 b2407 b3236 b1982 b3616 b3589 b3946 b2210 b0825 b4381 b2406 b0112 b0114 b0529 b2492 b0904 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.346873 (mmol/gDw/h)
  Minimum Production Rate : 1.128066 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.170053
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.131329
  EX_pi_e : 2.590727
  EX_so4_e : 0.087350
  EX_k_e : 0.067707
  EX_fe2_e : 0.005571
  EX_mg2_e : 0.003009
  EX_cl_e : 0.001805
  EX_ca2_e : 0.001805
  EX_cu2_e : 0.000246
  EX_mn2_e : 0.000240
  EX_zn2_e : 0.000118
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 48.660914
  EX_co2_e : 26.521410
  EX_h_e : 8.269711
  EX_pyr_e : 2.825323
  Auxiliary production reaction : 1.128066
  EX_acald_e : 0.305216
  EX_alltn_e : 0.000233
  DM_mththf_c : 0.000155
  EX_glyc__R_e : 0.000116
  DM_5drib_c : 0.000078
  DM_4crsol_c : 0.000077

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 21-Sep-2023
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